One misspelling that continues to baffle me is lose/loose. This isn't the obscure apostrophe nightmare that one finds with, say the word "it". Lose, loose. Sounds different, spelled different, you have to type extra letters to misspell "lose".
I would love it if somebody could explain how this particular misspelling happens, but I suppose that the thought processes involved are so low-level that there's no hope of explanation - much like when you accidentally start typing a different word, and then you wonder what word it was that your fingers were going to type.